Article
Biochemistry & Molecular Biology
Naomichi Takemata, Stephen D. Bell
Summary: Chromosome conformation capture technologies have identified topologically associating domains and A/B compartments as key features of eukaryotic chromosomes, with Sulfolobus archaea chromosomes also showing unique characteristics. The study reveals local rules governing the organization of topological domains and provides insights into the evolution of eukaryotic chromosome conformation through analysis of prokaryotic chromosome structures.
Article
Biochemical Research Methods
Carolyn N. Bayer, Ana G. V. Sepulchro, Maja Rennig, Morten H. H. Norholm
Summary: Engineering of bacterial genomes is an important technique in contemporary biotechnology, allowing for precise editing of chromosomes to develop cells with specific phenotypes and to create minimized genomes. The tetAOPT dual-selection marker is an optimized and easy-to-use genetic tool that can be efficiently utilized for genome engineering at different stages of the central dogma of molecular biology. It enables scarless knockouts and recombinant gene integrations on the DNA level, as well as advanced genome engineering of gene translation and transcription on the RNA and protein level.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Microbiology
Nicole Pearcy, Yue Hu, Michelle Baker, Alexandre Maciel-Guerra, Ning Xue, Wei Wang, Jasmeet Kaler, Zixin Peng, Fengqin Li, Tania Dottorini
Summary: The study focuses on the identification of genetic determinants associated with antimicrobial resistance in E. coli using a computational approach that integrates machine learning with metabolic modeling. The findings reveal key genetic determinants linked to growth and metabolic adaptations, providing insights into the complex interplay between antibiotic resistance and metabolic rewiring in bacteria. This computational solution has the potential to be applied to other human and animal pathogens for further studies on antimicrobial resistance.
Article
Biochemistry & Molecular Biology
Shengjian Yuan, Juan Shi, Jianrong Jiang, Yingfei Ma
Summary: The CRISPR/Cas9-based iterative phage genome reduction (CiPGr) approach was used to reduce the genomes of four distinct phages, resulting in heterogeneous genome-reduced mutants. Loss of non-essential genes for phage propagation was identified, although it had detrimental effects on phage fitness. However, some mutants showed higher infectious efficiency than their parental strains, indicating a trade-off between genome reduction and infectious fitness for phages. This study provides a foundation for future phage synthetic biology research leveraging CiPGr.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Jinzhao Long, Juna Geng, Yake Xu, Yuefei Jin, Haiyan Yang, Yuanlin Xi, Shuaiyin Chen, Guangcai Duan
Summary: In this study, a large-scale phylogenetic analysis of Shiga toxin-producing Escherichia coli (STEC) O26 strains was conducted. A new genetic Glade, ST29C4, was identified and was found to be in an intermediate phylogenetic position between ST29C3 and other non-ST29C3 strains. Furthermore, the ST29C4 strains were found to harbour virulence genes associated with both extraintestinal pathogenic E. coli (ExPEC) and STEC, suggesting the emergence of a hybrid pathogen with potential risk to human health.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemical Research Methods
Axel von Kamp, Steffen Klamt
Summary: In this study, a method is presented to modify the stoichiometry of the biomass reaction in order to make the flux balance analysis problem feasible and improve the accuracy of the model. Realistic flux measurements of E.coli are used to demonstrate the value of this approach, highlighting the overestimation of growth-associated maintenance (GAM) demand of ATP in recent genome-scale models.
Article
Infectious Diseases
Juan Li, Yuqin Song, Jianping Deng, Zhaoran Wang, Nai-Kei Wong, Chao Wang, Gang Zhang, Yang Wang, Shan Lu, Jie Che, Xiaofei Zhao, Zhengdong Zhang, Hong Wang, Ling Zhang, Yunfei Zhang, Xuemei Bai, Min Yuan, Xia Chen, Wen Zhang, Yanwen Xiong, Biao Kan, Jie Feng
Summary: This study explores the dynamics of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) transmission between food-producing animals and humans. The findings suggest that transmission primarily occurs through the high exposure group, which plays a crucial role as a medium, and the carriage rates of shared ARGs are higher in this group compared to the low exposure group.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Biology
Qingqing Fang, Yu Feng, Alan McNally, Zhiyong Zong
Summary: Fang et al. identified two previously unidentified phages that can inhibit the growth and decrease the virulence of carbapenem-resistant Klebsiella pneumoniae (CRKP). They also found that CRKP can develop phage resistance but can still be eliminated in a mouse intestinal colonization model, highlighting the potential of phage therapy as a treatment against drug-resistant pathogens.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Xue Yang, Zhitao Mao, Xin Zhao, Ruoyu Wang, Peiji Zhang, Jingyi Cai, Chaoyou Xue, Hongwu Ma
Summary: In this paper, a novel method integrating enzymatic and thermodynamic constraints is proposed for constructing a metabolic model of E. coli, demonstrating the potential application of metabolic models with multiple constraints for accurate pathway analysis and phenotype prediction.
METABOLIC ENGINEERING
(2021)
Article
Infectious Diseases
Antonella Santona, Jose Joao Sumbana, Maura Fiamma, Massimo Deligios, Elisa Taviani, Samuel Elija Simbine, Tomas Zimba, Jahit Sacarlal, Salvatore Rubino, Bianca Paglietti
Summary: ESBL-producing ExPEC, including high-risk lineages, were identified in extraintestinal infections at Maputo Central Hospital. The majority of isolates showed multidrug resistance, with ESBL genes associated with resistance to cefotaxime and ceftazidime. Furthermore, different sequence types were found to carry CTX-M transposition units, potentially facilitating the dissemination of ESBL genes. Genomic analysis revealed a diverse array of virulence-associated genes and clonality among isolates, suggesting the presence of hospital-acquired infections and long-term persistence.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2022)
Review
Biotechnology & Applied Microbiology
Jens Nielsen, Christian Brix Tillegreen, Dina Petranovic
Summary: Microbial fermentation plays a crucial role in sustainable production of food, chemicals, and natural products, with significant potential in new start-ups.
TRENDS IN BIOTECHNOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Zhenke Wu, Xiqin Liang, Mingkai Li, Mengyu Ma, Qiusheng Zheng, Defang Li, Tianyue An, Guoli Wang
Summary: Central carbon metabolism (CCM), which includes glycolysis, tricarboxylic acid cycle and the pentose phosphate pathway, is crucial for maintaining normal cellular growth. In recent years, CCM has been widely used in microbial metabolic engineering due to its regulatory role in cellular metabolism. This study summarizes the strategies for optimizing CCM in eukaryotic and prokaryotic microbial chassis, such as introducing heterologous CCM pathways and optimizing key enzymes or regulatory factors, and explores the bottlenecks and future prospects of CCM optimization in metabolic engineering.
MICROBIAL CELL FACTORIES
(2023)
Article
Multidisciplinary Sciences
Wen Sun, Ke Yang, Risheng Li, Tianqing Chen, Longfei Xia, Zhao Wang, Xubo Sun
Summary: This research analyzed the structure of a microorganism group in sediment and the absolute abundance of two typical pathogenic bacteria in Shahe Reservoir, China. The results show a positive correlation between the abundance of pathogenic bacteria and water eutrophication in the reservoir sediment. Additionally, the distribution of the pathogenic bacteria varies with depth and location in the sediment.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Aidin Behravan, Atieh Hashemi, Sayed-Amir Marashi, Hamideh Fouladiha
Summary: In this study, a genome-scale metabolic modeling approach was used to identify gene targets for improving the production of antiEpEX-scFv in E. coli. The modeling predictions were validated by overexpressing a target gene in the parent strain, which led to increased scFv production. This study highlights the potential of genome-scale metabolic modeling for enhancing the production of recombinant proteins.
BIOTECHNOLOGY LETTERS
(2022)
Article
Biochemical Research Methods
Yu Kang, Lina Yuan, Xing Shi, Yanan Chu, Zilong He, Xinmiao Jia, Qiang Lin, Qin Ma, Jian Wang, Jingfa Xiao, Songnian Hu, Zhancheng Gao, Fei Chen, Jun Yu
Summary: This study investigates genome-wide recombination within a species using a dataset of Escherichia coli genomes. The research highlights extensive within-clade recombination and a sharp decline in between-clade recombination, establishing a genetic barrier between clades as phylogenetic distance increases. Recombination plays a critical role in early speciation by optimizing genes and alleles for physiological activities and shaping genetic diversity within populations.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Philipp Schneider, Axel von Kamp, Steffen Klamt
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Simon Boecker, Bjoern-Johannes Harder, Regina Kutscha, Stefan Pfluegl, Steffen Klamt
Summary: Enforced ATP wasting through overexpressing the genes of the ATP-hydrolyzing F-1-part of the ATPase significantly increased the yield and productivity of 2,3-BDO synthesis in E. coli. The ATPase strain outperformed the control strain in specific substrate uptake and 2,3-BDO synthesis rate, leading to the design of a three-stage process for optimal glucose to 2,3-BDO conversion with high productivity and yield.
MICROBIAL CELL FACTORIES
(2021)
Article
Biochemical Research Methods
Philipp Schneider, Radhakrishnan Mahadevan, Steffen Klamt
Summary: This paper proposes an ontology for different degrees of growth-coupled product synthesis and extends the Minimal Cut Sets (MCS) framework to allow computation of designs for all GCP classes within a single framework. The study illustrates hierarchical relationships between coupling degrees and shows that feasibility of coupling is not affected by the chosen GCP degree. The principle of coupling can be generalized to couple product synthesis with other cellular functions beyond growth.
BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Pavlos Stephanos Bekiaris, Steffen Klamt
Summary: Microbial communities are crucial for biogeochemical cycles, biomedicine, and biotechnological applications. While naturally arising communities are used in some processes, the design of synthetic microbial consortia for bio-based production has gained interest. A new computational approach, ASTHERISC, has been developed to design single-species multi-strain communities for maximizing thermodynamic driving force for product synthesis. This approach shows potential for improving microbial community design for chemical production.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Engineering, Chemical
Sebastian Espinel-Rios, Katja Bettenbrock, Steffen Klamt, Rolf Findeisen
Summary: The paper presents a constrained model-based optimization and predictive control framework to maximize the production efficiency of batch fermentations by manipulating ATP wasting. By formulating ATP wasting as a model-based optimal control problem, the trade-offs between product yield and volumetric productivity can be balanced. The approach incorporates moving horizon model predictive control and constraint-based dynamic modeling to overcome model-plant mismatch, disturbances, and uncertainties.
Article
Biochemical Research Methods
Sven Thiele, Axel von Kamp, Pavlos Stephanos Bekiaris, Philipp Schneider, Steffen Klamt
Summary: CNApy is an open-source desktop application written in Python that offers a graphical interface for analyzing metabolic networks. It supports various COBRA techniques and allows for easy extension of functionalities.
Article
Biochemistry & Molecular Biology
Simon Boecker, Giulia Slaviero, Thorben Schramm, Witold Szymanski, Ralf Steuer, Hannes Link, Steffen Klamt
Summary: This study systematically analyzed the impact of different ATP demands on glycolytic flux in Escherichia coli, revealing a biphasic behavior induced by the dual dependency of phosphofructokinase on ATP and ADP. The results provide insights into fundamental mechanisms of bacterial energy metabolism and offer guidance for the rational design of highly productive cell factories. Model analysis confirmed major rate-controlling steps in glycolysis under high ATP demand, which were experimentally validated.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Simon Boecker, Sebastian Espinel-Rios, Katja Bettenbrock, Steffen Klamt
Summary: A novel strategy for fermentative growth of Escherichia coli on glycerol in defined minimal medium was proposed and validated through model-based calculations. The strategy involved the uptake of small amounts of acetate with subsequent reduction to ethanol, which enabled redox balance in the anaerobic conditions. The study also generated an E. coli strain that exhibited robust growth, high glycerol uptake rate, and near-maximum ethanol yield, offering new perspectives for sustainable production processes based on glycerol.
METABOLIC ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Steffen Klamt, Axel von Kamp
Summary: Flux balance analysis (FBA) is a crucial method for analyzing metabolic networks, but it may encounter infeasible scenarios. This article presents and compares two methods, based on linear programming (LP) and quadratic programming (QP), to address the infeasibility of FBA problems. The authors provide practical guidance on handling infeasible FBA systems and discuss relevant examples. Additionally, they highlight the relationships to classical metabolic flux analysis.
Article
Biochemical Research Methods
Philipp Schneider, Pavlos Stephanos Bekiaris, Axel von Kamp, Steffen Klamt
Summary: This article introduces a Python package called StrainDesign, which is built upon the COBRApy toolbox and integrates various metabolic design algorithms. The package provides advanced features and enhanced tools for analyzing computed intervention strategies.
Article
Biochemical Research Methods
Gerrich Behrendt, Jonas Frohwitter, Maria Vlachonikolou, Steffen Klamt, Katja Bettenbrock
Summary: Zymo-Parts is a modular toolbox based on Golden-Gate cloning that enables efficient construction of genetically modified strains. It offers a collection of promoters, terminators, ribosomal binding sites, and reporter genes for achieving desired levels of gene expression. The GoldenBraid-based system allows for the assembly of operons with multiple genes. The utility of Zymo-Parts for metabolic engineering applications is demonstrated by overexpressing a heterologous lactate dehydrogenase gene in Z. mobilis.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Julian Wichmann, Gerrich Behrendt, Simon Boecker, Steffen Klamt
Summary: This study systematically tested and characterized 15 promoter candidates that are induced upon oxygen depletion in Escherichia coli. Six of these promoters are particularly suited for dynamic metabolic engineering applications. The study also demonstrated the optimization of a two-stage lactate production process using these promoters.
METABOLIC ENGINEERING
(2023)
Article
Multidisciplinary Sciences
Pavlos Stephanos Bekiaris, Steffen Klamt
Summary: The study presents a computational framework to analyze the impact of redox cofactor swaps on the thermodynamic potential of a metabolic network. It suggests that the specificity of NAD(P)H reactions is influenced by the metabolic network structure, enabling thermodynamic driving forces close to the theoretical optimum.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Sebastian Espinel-Rios, Bruno Morabito, Johannes Pohlodek, Katja Bettenbrock, Steffen Klamt, Rolf Findeisen
Summary: Biotechnology provides opportunities for sustainable production of valuable products. Optimization tools include both extracellular process elements and intracellular metabolic and genetic engineering methods. The concept of cybergenetics coupled with model-based optimization and predictive control enables online modulation of gene expression and feedback control to achieve optimal performance in dynamic bioprocesses. Fed-batch processes and substrate feeding rate optimization are used as examples to demonstrate the application of these methods.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biochemical Research Methods
Axel von Kamp, Steffen Klamt
Summary: In this study, a method is presented to modify the stoichiometry of the biomass reaction in order to make the flux balance analysis problem feasible and improve the accuracy of the model. Realistic flux measurements of E.coli are used to demonstrate the value of this approach, highlighting the overestimation of growth-associated maintenance (GAM) demand of ATP in recent genome-scale models.